Brain tumor targeting peptides and methods

ABSTRACT

A method of diagnosing and treating a human glioblastoma multiforme (GBM) brain tumor in a subject is disclosed. The method includes administering to the subject, an effective amount of composition having a peptide 12-20 amino acid residues in length and selected for its ability to bind preferentially to a subtype of human GBM cells identified as brain tumor initiating cells (BTICs) or highly invasive glioma cells (HIGCs).

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of U.S. application Ser. No.12/950,855, filed Nov. 19, 2010, which claims the benefit of U.S.Provisional Application No. 61/264,064, filed Nov. 24, 2009, both ofwhich are incorporated herein by reference in their entirety.

FIELD OF THE INVENTION

The present invention relates to the field of peptides capable oftargeting malignant glioma cells, and in particular, a brain tumorinitiating cell (BTIC) subtype of human glioblastoma multiforme (GBM)cells and highly invasive glioma cell (HIGC) subtype of human GBM cells,and to methods employing the peptides.

REFERENCES

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BACKGROUND OF THE INVENTION

Glioblastoma multiforme (GBM) is a complex and heterogeneous disease,with prevalent short-term relapse and a median survival time of about 1year when treated with surgery, radiotherapy and temozolomide [1-3].Categorization by transcriptional clustering into proneural (betterpatient survival profile), indeterminant (“neural”), mesenchymal(associated with NF-1 loss) and proliferative (“classical”; associatedwith EGFR mutation or amplification) subtypes (reviewed in [1]) hasunderscored the usefulness of individualized patient profiles indetermining prognosis as well as rational selection of targetedtherapeutics, however a practical approach to targeting these subtypesclinically needs to be developed.

Despite intensive radio- and chemotherapy, tumor regrowth is virtuallyinevitable and typically occurs within a few centimeters of theresection margin [4]. There are two potential disease reservoirs thatmay contribute to treatment failure. First, invasive glioma has beencharacterized by recent clinical and in vitro studies which have shownthat genetically and phenotypically distinct cells can form longtendrils which extend several centimeters away from the main tumor mass,or form diffusely spread, invasive subpopulations of tumor that areresistant to chemo- and radiotherapy, by virtue of their remotelocalization from the main tumor site [4-6], as well as expression ofdrug resistance genes and enhanced DNA repair capabilities [7-10]. Thesecells are referred to herein as highly invasive glioma cells, or HIGC's.

The second putative reservoir is based on concept of Cancer Stem Cells(CSCs), which arose because mechanisms of self-renewal without terminaldifferentiation were similar between stem cells and cancer cells [11].The cancer stem cell hypothesis proposes that a rare population oftransformed stem cells, or progenitor cells with acquired self-renewalproperties are the source of tumor cell renewal. Evidence for theexistence of cancer stem cells has been suggested for a number ofhematological malignancies [12-14] and more recently for a number ofsolid tumors [14-18].

There is now accumulating in vitro and in vivo data supporting theinvolvement of CSCs in glioblastoma [19-25]. The concept of brain tumorstem cells, or as they are referred to herein, as brain tumor-initiatingcells or BTICs, is potentially important since they would define atumor's behavior including proliferation, progression and response totherapy. One of the most important features of BTICs is that theyclosely resemble the human disease and therefore may be the best systemfor understanding brain tumor biology and developing therapeutics [23].In addition, BTICs have fewer cytogenetic and molecular abnormalities[21, 23], which should make identifying causal events (i.e. instead ofchanges which occur as a consequence of transformation) in brain tumorformation easier. It should be clearly stated that the presence of aBTIC and the exact operational definition and use of terminology is atopic of great debate. As CD133 is controversial as an indicator of“sternness” [26-28], it is proposed herein that BTICs be defined aspatient-derived cells with the ability to self-renew, differentiate intomultiple lineages and form tumors in vivo [28].

SUMMARY OF THE INVENTION

The invention includes, in one aspect, a peptide composition fortargeting one of (i) a highly invasive glioma cell (HIGC) subtype ofhuman glioblastoma multiforme (GBM) cells characterized by their abilityto migrate from one brain hemisphere into which the cells are injectedinto the contralateral hemisphere, and (ii) a brain tumor initiatingcell (BTIC) subtype of human GBM cells characterized by their stem-celllike properties of being able to self renew, generate spheres withoutthe addition of exogenous mitogens and growth factors, and induce tumorformation in vivo when placed in the brains of immunocompromised mice.The composition includes an isolated peptide of between 12-20 aminoacids and containing a sequence selected from the group consisting ofSEQ ID NOS: 1-10, 13, and 17 for targeting HIGCs, and SEQ ID NOS: 11-16,for targeting BTICs.

The composition may include multiple GMB-binding peptides, for example,at least one peptide that binds preferentially to HIGC's and at leastone peptide that binds preferentially to BTIC's.

The peptide of the composition may be composed of L-amino acids, D-aminoacids, a mixture of L- and D-amino acids, or a retro-inverso peptideformed of D-amino acids arranged in reverse order.

For use in localizing of HIGCs or BTICs in a subject with a human GBMtumor, the composition may include a contrast agent coupled to thepeptide.

For use in inhibiting or killing HIGCs or BTICs in a subject with ahuman GBM tumor, the composition may further include an anti-tumor agentcoupled to the peptide.

For use in targeting HIGCs, the peptide may contain a sequence selectedfrom the group consisting of SEQ ID NOS: 7 (H10), 13 (E10) and 17(modified H10), and preferably SEQ ID NOS: 17 (modified H10).

For use in targeting BTICs, the peptide may contain a sequence selectedfrom the group consisting of SEQ ID NOS: 11 (7A), 14 (3F), 16 (3B), and13 (E10), and preferably SEQ ID NOS: 11 (7A).

For use in delivery to a patient human GBM tumor across the blood-brainbarrier, the isolated peptide may be coupled to a carrier peptide havingthe sequence identified by SEQ ID NOS: 18 or 19, and in anotherembodiment, may be encapsulated within a nanoparticle formed ofpoly(lactide-co-glycolide) copolymer, a cyclodextrin, or cetylalcohol/polysorbate.

Also disclosed is the use of the above peptide composition for detectingthe presence of HIGC or BTIC subtypes of cells in a patient with a humanGBM tumor, where the composition includes a detectable contrast agentcoupled to the peptide. The peptide in an exemplary composition fordetecting the presence of an HIGC subtype of cells contains the sequenceSEQ ID NO: 7 or 17, and may additionally include the peptide identifiedby SEQ ID NO: 18 or 19. The peptide in an exemplary composition fordetecting the presence of a BTIC subtype class of cells contains thesequence SEQ ID NO: 11, and may additionally include the peptideidentified by SEQ ID NO: 18 or 19.

Further disclosed is the use of the above peptide composition, forinhibiting or killing HIGC or BTIC subtypes of cells in a patient with ahuman glioblastoma multiform (GBM) tumor, where the composition includesan anti-tumor agent coupled to the peptide. The peptide in one exemplarycomposition for inhibiting or killing an HIGC subtype of cells containsthe sequence SEQ ID NO: 7 or 17. The peptide in an exemplary compositionfor inhibiting or killing a BTIC subtype of cells contains the sequenceSEQ ID NO: 11.

In another aspect, the invention includes a method of characterizing aglioblastoma multiforme (GBM) tumor in a patient, by the steps of:

(a) generating an image of the patient's brain tumor after administeringto the patient a peptide composition containing (i) a first peptidehaving between 12-20 amino acids in length that has been selected forits preferential binding to a highly invasive glioma cell (HIGC) subtypeof human GBM cells characterized by their ability to migrate from onebrain hemisphere into which the cells are injected into thecontralateral hemisphere, and coupled to first peptide, a first contrastagent that allows the first peptide, when bound to cells in the patienttumor region, to be imaged in vivo;

(b) generating an image of the patient's brain tumor after administeringto the patient a peptide composition containing (i) second peptidehaving between 12-20 amino acids in length that has been selected forits preferential binding to a brain tumor initiating cell (BTIC) subtypeof human GBM cells characterized by their stem-cell like properties ofbeing able to self renew, generate spheres without the addition ofexogenous mitogens and growth factors, and induce tumor formation invivo when placed in the brains of immunocompromised mice, and coupled tothe second peptide, a second contrast agent that allows the secondpeptide, when bound to cells in the patient tumor region, to be imaginedin vivo; and

(c) determining, from the distribution of the first and second peptidesand their associated contrast observed in the image(s) generated insteps (a) and (b), at least one of:

(ci) the boundaries of the tumor, for purposes of surgical resection ofthe tumor,

(cii) the boundaries of the tumor for purposes of radiation therapy ofthe tumor,

(ciii) the expression profiles of different tumor-cell phenotypes withinthe tumor, for purposes of tailoring a chemotherapeutic regimen fortreating the tumor; and

(civ) the change in the distribution of the first and second peptidesand their associated contrast agents over a given time course in whichsteps (a) and (b) are repeated over time.

Steps (a) and (b) may be carried out by one of:

(i) MRI, wherein the contrast agent is selected from the groupconsisting of a gadolinium-based contrast agent, an iron oxide contrastagent, and a manganese contrast agent;

(ii) positron emission tomography (PET) or scintigraphy, wherein thecontrast agent is selected from the group consisting of ⁶⁴Cudiacetyl-bis(N⁴-methylthiosemicarbazone), ¹⁸F-fluorodeoxyglucose,¹⁸F-fluoride, 3′-deoxy-3′-[¹⁸F]fluorothymidine (FLT),¹⁸F-fluoromisonidazole, gallium, Technetium-99m, and thallium; and

(iii) x-ray imaging, where the contrast agent is selected from the groupconsisting of barium, gastrografin, and iodine contrast agents.

The peptide compositions may be administered intravenously. In oneembodiment, steps (a) and (b) are carried out together, and the firstand second contrast agents allow the distributions of bound first andsecond peptides to be independently determined. In another embodiment,(a) and (b) are carried sequentially.

The first peptide administered may contain a sequence selected from thegroup consisting of SEQ ID NOS: 7 (H10), 13 (E10) and 17 (modified H10).The second peptide administered may contain a sequence selected from thegroup consisting SEQ ID NOS: 11 (7A), 13 (E10), 14 (3F) and 16 (3B).

In yet another aspect, the invention includes a method of characterizingthe gene expression profiles of cellular phenotypes in a humanglioblastoma multiforme (GBM) tumor in a patient, by the steps of:

(a) identifying cells in the tumor corresponding to one of (i) adifferentiated GBM tumor cell, (ii) a highly invasive glioma cell (HIGC)subtype of human glioblastoma multiforme (GBM) cells characterized bytheir ability to migrate from one brain hemisphere into which the cellsare injected into the contralateral hemisphere, and (iii) a brain tumorinitiating cell (BTIC) subtype of human GBM cells characterized by theirstem-cell like properties of being able to self renew, generate sphereswithout the addition of exogenous mitogens and growth factors, andinduce tumor formation in vivo when placed in the brains ofimmuno-compromised mice, and

(b) correlating the identified cell type with the known gene expressionpattern of that cell type.

These and other objects and features of the invention will become morefully apparent when the following detailed description of the inventionis read in conjunction with the accompanying figures.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A is a schematic paradigm for the selection of phage that boundpreferentially to the highly invasive glioma cell population developedby in vivo serial passage referred to as U87R. Peptide selection wasperformed in a two-step process using a series of biopanning steps wherethe PhD-12 M13 combinatorial phage display library was first subtractedfor phage that bound to non-target cells, the non-invasive U87T cells,to remove any phage common between the cell types. Next, a positiveselection was performed for phage that bound preferentially to thetarget cells, U87R. Any non-bound phage was discarded and the remainingphage were amplified in a series of steps that enriched for the targetspecific phage referred to as the 12R library.

FIG. 1B shows a whole cell ELISA assay that detects phage that is boundto the surface of the cells. The 12R phage library was incubated withthe invasive U87R or non-invasive U87T cells, any non-bound phage wereremoved and an HRP-anti-M13 antibody and TMB substrate (blue) was usedto detect bound phage. The 12R library preferentially bound to thehighly invasive U87R cells.

FIG. 2A illustrates the inhibitory ability of the 12R library subcloneH10 to selectively inhibit glioma invasion. Plating serial dilutions ofphage with host bacteria on agarose plates was used to isolate phagesubclones. Individual clones were isolated, amplified and tested fortheir inhibitory ability in in vitro invasion assays. The phagedesignated as H10 specifically and significantly blocked the migrationof the invasive U87R cells through brain-like matrix coated transwellmembranes (3×10¹⁰ pfu; 4 hrs at 37° C.). Assessing the effects of LPS orrandom phage controlled for potential contamination by the hostbacterial culture;

FIG. 2B shows that in addition to the H10 phage, the H10 syntheticpeptide (50 uM) effectively and selectively inhibits migration of thehighly invasive U87R cells, as well as the U87MG cells transfected withp75^(NTR), a protein shown to mediate glioma invasion;

FIG. 2C demonstrates the clinical relevance of the H10 peptide, as themigration of 3/5 (60%) brain tumor initiating cell (BTIC) isolates fromglioblastoma patients were inhibited by the H10 peptide. Asterisksindicate a statistically significant difference from untreated control;Dunnett's test (p<0.05);

FIG. 3A is a bar graph showing that cholesterol oxidase inhibits cellmigration. The invasive U87R cells were plated on matrix-coatedtranswell membranes and treated with cholesterol oxidase (1.8 U/mL) for4 hours. Cells that migrated to the underside of the transwell membranewere stained with crystal violet and counted by light microscopy;

FIG. 3B shows that cholesterol oxidase prevents internalization of alipid raft marker GM1. U87R cells were plated onto matrix-coatedtranswell membranes and treated with cholesterol oxidase and Alexa555-cholera toxin B subunit for 120 minutes to assess differences in theuptake and/or turn over of its receptor, GM1. The white arrow indicatesa membranous accumulation of GM1;

FIG. 4A shows accumulation of GM1 in the presence of H10. Invasive U87Rcells were plated onto matrix-coated transwell membranes and incubatedwith H10 phage in the presence of Alexa 555-cholera toxin B subunit for30 minutes to assess differences in the uptake and/or turn over of thelipid raft marker GM1. Cells treated with H10 showed a generalizedaccumulation of GM1 staining, characterized by globular internalstructures and membranous localization (white arrows);

FIG. 4B are western blots showing that treatment of invasive gliomacells with H10 or cholesterol oxidase results in the accumulation ofhigher molecular weight complexes of p75^(NTR), a membrane protein foundin lipid rafts and known to promote cell migration. Density gradientfractions were prepared from U87R cells plated onto collagen and treatedwith PBS (control), H10 phage, F2 phage, or cholesterol oxidase for 2hours, and analyzed by Western Blot for p75^(NTR). White arrows indicatehigher molecular weight p75^(NTR)-containing complexes. Lines underneaththe figure indicate the fractions in which common organelles aregenerally found;

FIG. 4C shows that treatment of glioma cells with H10 results inaccumulation of p75^(NTR) at the plasma membrane. BTIC 25 cells (no GFP)were plated on matrix-coated transwell membranes and treated with phagefor 2 hours. The p75^(NTR) receptor, which is normally cleaved duringp75^(NTR) signaling, is greatly increased at the cell membrane after H10treatment. p75^(NTR) does not appear to accumulate in the H10-affectedGM1 compartment, suggesting H10 may act on more than one class ofmembrane structure;

FIG. 5 shows single Z-stack projections from confocal micrographs ofBTIC isolates stained with biotinylated 7A peptide. Binding specificityof the 7A peptide was assessed with non-target (U87MG; NSC) and target(BTIC) cells using a biotinylated 7A peptide (red) followed by confocalimaging.

FIG. 6A illustrates the in vivo homing capability of H10. Invasive U87Ror non-invasive U87T cells were grown in the right brain hemisphere ofSCID mice. Once tumors were established, mice were anaesthetized andperfused with H10 phage for 10 minutes. Unbound phage was flushed fromthe system with PBS. Brains were cryosectioned and immunohistochemicallystained for M13 phage or human nuclear antigen (hNA). In comparison tothe tumors established using the U87T cells, the H10 phage homed moreefficiently to the U87R tumor cells as demonstrated by increasedstaining on the U87R cell bodies and along the edge of the xenograftmass.

FIG. 6B shows that 7A homes in vivo to BTIC12 and BTIC25 xenografts.Cells were injected into the right brain hemisphere of SCID mice andallowed to establish for three months. Mice were then perfused with 7Aor Al (random control) phage for 10 minutes. The distribution of phagebinding was unique between the two BTIC xenografts and again revealsheterogeneity within the samples. 7A homing was not observed in micebearing tumors generated from the U251N cell line. Perfusion of a BTIC25 xenograft with a randomly selected phage, Al, showed minimalstaining;

FIG. 7 demonstrates that the 7A peptide can distinguish subpopulationswithin a BTIC isolate with defined cellular behavior. BTIC25 wassubcloned by limiting dilution and screened for binding to biotinylated7A peptide (red). Subpopulations that bound to 7A had a higherpropensity to form neurospheres in culture, were not highlyproliferative as a xenograft in SCID mice, and were found preferentiallynear the ventricles. Human xenografts were implanted in the right brainhemisphere of mice and visualized by an antibody to a human nuclearantigen (brown). Sections were counterstained with Toluidine blue tovisualize all cell nuclei.

FIG. 8 is a table showing binding specificities of BTIC-selectivepeptides on a representative selection of BTIC isolates;

FIG. 9A are confocal images of p75^(NTR) transfected glioma cells(U87p75) imaged for uptake of FITC-transferrin. U87p75^(NTR) grown inthe presence of H10 and cholesterol oxidase were assessed forFITC-transferrin uptake 2 hours after cells were plated oncollagen-coated transwell membranes. H10 and cholesterol oxidase had noeffect on distribution of transferrin or transferrin receptor, markersof clathrin-coated vesicles;

FIG. 9B shows cellular fractionation of invasive U87R cells usingiodixanol gradient separation. U87R cells were treated with H10, F2,cholesterol oxidase or control PBS for two hours. Cells were lysed,fractioned using an iodixanol gradient, and Western Blot analysis forthe transferrin receptor was performed;

FIG. 10A shows an anti-p75^(NTR) Western blot and full-length p75^(NTR),the C-terminal fragment (a-secretase) and intracellular domain(γ-secretase) cleavage products were visualized after treatment withH10, MbCD or H10+MbCD;

FIG. 10B shows Western Blot analysis of full-length p75^(NTR) afterexposure to H10 for 4 hours and 1 week;

FIG. 10C shows in vitro invasion assays performed in the presence ofcholesterol oxidase and methyl-β-cyclodextran. Both cholesterol oxidaseand methyl-β-cyclodextran significantly inhibited cell migration ofU87p75 glioma cells;

FIG. 11 shows confocal images of a panel of patient-derived BTICisolates (rows) that have been screened for binding specificity to anumber of biotinylated synthetic peptides (red; columns).

FIGS. 12A and 12B show in vitro transwell migration assays in thepresence of different extracellular matrices. The presence of brainmatrix was essential for H10-mediated abrogation of cell migration invitro (FIG. 12A), with collagen I mediating the majority of the effect(FIG. 12B).

FIGS. 13A and 13B are high magnification images of thin sections fromfive mouse brains that were bisected close to a tumor-implantation site(13A), and stained with biotinylated 7A peptide, and thin sections fromfive mouse brains injected with non-7A binding subclones (13B);

FIG. 14A shows the ability of fluorescently labeled 7A peptide to homein a live mouse to a large implanted tumor grown from BT025 cells (14A).FIGS. 14B and 14C are lower and higher magnifications, respectively, ofthin sections taken from the brain in FIG. 14A after it was bisectedclose to the tumor implantation site and stained for human nuclearantigen (green) and total DNA (blue) to outline the positioning of thecells. The red peptide signal is visible on cells immediately adjacentto the main tumor mass as well as spread diffusely in the surroundingtissue.

FIG. 15A shows an intact mouse brain carrying a BT025-implanted tumor,after the mouse was injected via the carotid artery with fluorescentlytagged 3B peptide; FIG. 15B is a fluorescently stained thin section ofthe brain in 15A, showing that the red peptide signal is both within andoutside of the main tumor mass;

FIG. 16A shows am intact mouse brain bisected at the tumor injectionsite and cut sides turned upwards; FIGS. 16B and 16C are lower andhigher magnification photomicrograghs, respectively, of brain sectionsfrom animals who received intracarotid injection of the 3F peptide,showing that 3F binds primarily to cells that are diffusely spreadoutside the main tumor mass;

FIGS. 17A and 17B show that similar results to those seen in FIGS. 16Band 16C can be when the peptide is administered by tail vein injectionrather than intracarotid injection;

FIG. 18A shows a whole mouse brain and the site to tumor injection;FIGS. 18B and 18C are photomicrographs of brain sections from animalswho received intracarotid injections of the H10 peptide, showing thatH10 binds primarily to cells that are diffusely spread outside of themain tumor mass; FIG. 18D shows a similar result when the peptide isadministered by tail vein;

FIG. 19A shows a whole mouse brain and the site to tumor injection;FIGS. 19B and 19C are photomicrographs of brain sections from animalswho received intracarotid injections of the E10 peptide, showing thatE10 binds to a portion of cells within the tumor mass (19B), and tocells outside the main tumor mass (19C); Similar results were observedwhen the E10 peptide was injected via the tail vein (FIG. 19D); and

FIG. 20 shows gene clustering of microarray data generated from mRNAisolated from three independently isolated 7A binding cell subclones andthree independently isolated 7A non-binding subclones.

DETAILED DESCRIPTION OF THE INVENTION I. Definitions

“Human glioblastoma multiforme (GBM)” refers to the most common andaggressive type of primary brain tumor in humans. GBM tumors arecharacterized by the presence of small areas of necrotizing tissue thatis surrounded by anaplastic cells (pseudopalisading necrosis). Thischaracteristic, as well as the presence of hyperplastic blood vessels,differentiates the tumor from Grade 3 astrocytomas, which do not havethese features.

“Highly invasive glioma cells,” or “HIGCs,” are a subtype(subpopulation) of human GBM cells characterized by an ability tomigrate from one brain hemisphere into which the cells are injected intothe contralateral hemisphere. An example of an HIGC is the U87R subtypeof the U87MG human glioblastoma cells.

“Brain-tumor initiating cells,” or “BTICs,” are a subtype(subpopulation) of human GBM cells characterized by their stem-cell likeproperties of being able to self renew, generate spheres without theaddition of exogenous mitogens and growth factors, and induce tumorformation in vivo when placed in the brains of immuno-compromised mice.

“Peptide-displaying phage” refers to bacteriophage that have beenengineered to express a library, typically a combinatorial library, ofexogenous peptides on their surfaces, allowing phage selection based onthe presence on the phage surface of an exogenous library peptide.

“HIGC-specific peptides” refers to peptides, typically associated withpeptide-displaying phage, that bind preferentially to HIGCs under theconditions of phage-display panning described in Section VIIIC below.

“BTIC-specific peptides” are peptides, typically associated withpeptide-displaying phage, that bind preferentially to BTICs under theconditions of phage-display panning described in Section VIIID below.

Peptide-displaying phage “bind preferentially to HIGCs or BTICs” if thephage remain bound to immobilized HIGC or BTIC target cells under thephage-panning wash conditions described in Section VIIIC and VIIID,respectively, below.

Amino acid residues are indicated herein by their standard one-lettercode (see, for example, www.mun.ca/biochem/courses/3107/aasymbols.html).

A “contrast agent” refers to an imaging agent used in connection with animaging technique, such as magnetic resonance imaging (MRI), positronemission tomography (PET), scintigraphy, computed tomography (CT), andx-ray imagining, to enhance the information available from the image,particularly as it relates to the binding of the imaging agent to targetanatomical structures or cells. Exemplary contrast agents include (i)gadolinium-based contrast agents, iron oxide contrast agents, andmanganese contrast agents used in MRI; ⁶⁴Cudiacetyl-bis(N⁴-methylthiosemicarbazone), ¹⁸F-fluorodeoxyglucose,¹⁸F-fluoride, 3′-deoxy-3′-[¹⁸F]fluorothymidine (FLT),¹⁸F-fluoromisonidazole, gallium, Technetium-99m, and thallium, used inPET or scintigraphy; and barium, gastrografin, and iodine contrastagents used in x-ray imaging.

An agent is “coupled” to a peptide if it is attached directly orindirectly to the peptide in a manner that allows the agent to becarried with the peptide, e.g., in the bloodstream, as a stabletwo-component composition. The agent may be covalently coupled to thepeptide, or carried in a structure, such as a chelate, cavitand,nanoparticle, or lipid particle, which is itself covalently coupled tothe peptide, or may be carried with the peptide within a stablestructure, such as a nanoparticle or lipid structure.

II. U87R-Cell Specific Peptides

In accordance with the present invention, the invasive glioma and BTICcompartments have been newly modeled, allowing detailed examination ofpotential targetable components. The invasive glioma model describedherein was developed by in vivo serial passaging of GFP neo-transfectedU87MG human glioblastoma cells through mouse brains to isolate theinvasive subpopulation (U87R, remote from primary tumor) from brainhemispheres that were contralateral to the injection sites [5, 6]. Whencultured in vitro and compared to their non-invasive counterparts (U87T,tumor forming), these cells retained a higher propensity to invade bothin vitro and upon reinjection into mouse brains. Microarray analysesshowed that many genes were either down- or up-regulated in the U87Rcells when compared to the U87T cells, including increased expression ofp75^(NTR). Using a combination of functional, biochemical, and clinicalstudies, it was found that p75^(NTR) dramatically enhanced migration andinvasion of genetically distinct glioma cells and frequently exhibitedrobust expression in highly invasive glioblastoma patient specimens [6].These observations suggest that the U87R subpopulation is an appropriatemodel cell line for the subsequent peptide screening. The U87R subtypeis an example of a highly invasive glioma cell (HIGC).

The BTIC model consists of a series of primary cell cultures derivedfrom freshly resected human brain tumor specimens. Originating tumorsare tested against a routine panel of antibodies to confirm a diagnosisof GBM, then subpopulations are selected via their ability to formself-renewing neurospheres in culture, as well as differentiate intoastrocytic, oligodendrocytic or neuronal lineages. Upon injection of asfew as ten cells into mouse brains, these brain tumor initiating cells(BTICs) tend to recapitulate the primary tumor as well as robustlyinvade, similar to what is seen with clinical GBM specimens [28].Although it is unclear if BTICs are the best representation of braincancer stem cells, they remain an excellent model for delineating thebehavior of the human disease.

In accordance with the invention, peptides useful in targeting,characterizing and manipulating cells from disease reservoirs implicatedin relapse of post-treatment GBM have been identified. The peptideselection was accomplished through phage display techniques alreadyproven successful in other studies. For example, biopanning a phagedisplay library against target cells or purified molecules has led tothe characterization of cell surface proteins unique to defined cellsubpopulations (e.g. the vascular address system [30, 31]), theidentification of motifs important for specific protein function (e.g.the RGD motif necessary for integrin engagement [32-34]), as well as theisolation of peptide reagents with functional utility [35-38]. Inpractical terms, selection of unique phage displayed peptide sequencesuseful in diagnosis or therapy of patient glioblastomas can only be doneex vivo, necessitating the development of our unique, clinicallyrelevant model systems, which recapitulate particular characteristics ofGBM that cause therapeutic difficulties, allowing the causative celltypes to be studied in isolation.

The final panels of selected peptides described herein have shown to beuseful in demonstrating the molecular heterogeneity between cellpopulations and within a given cell population, and may lead to furtherrefinement in the characterization of glioblastoma subtypes which willallow matching of tumor phenotypes with patient outcome, or with aparticular therapeutic regimen, essential components of personalizedmedicine in cancer therapy. Alternately, because of the in vivo utilitydemonstrated, these peptides can be used as clinical imaging tools, orreagents for targeting chemotherapeutics to a particular tumor subtype.There is also inherent therapeutic potential of the unmodified peptides,as one of these dramatically inhibits the migration and invasiveabilities of U87R cells as well as patient isolates that exhibitinvasive properties.

A. Selective Biopanning of the Phage Display Library Resulted in theIsolation of a U87R-Specific Peptide Sequence that Inhibits Glioma CellMigration

The present inventors have earlier described an in vivo selection for apopulation of human glioma cells that were highly invasive (U87R) [6].In order to isolate peptides that could bind specifically to thesehighly invasive glioma cells, a biopanning experiment using acombinatorial phage display library was employed. Initially subtractivebiopanning was performed with the U87 cells that were non-invasive(U87T) followed by selective biopanning with the U87R cells to isolate alibrary of phage (FIG. 1A) that were confirmed to preferentiallyinteract with U87R cells by whole-cell ELISA (FIG. 1B). These phage weresubcloned by plating serial dilutions of phage with host bacteria onagarose plates, and the sequences of the peptide inserts weredetermined, and listed in Table 1, which shows, from left-to-right, (i)the peptide identifier, (ii) peptide sequence e, (iii) SEQ ID NO, and(iv) number cell-binding phages containing that sequence.

To select a phage subclone for further biochemical and in vivoevaluation, phage were tested for the ability to functionally affect thebehavior of the U87R cells. The H10 phage-displayed sequence (SEQ IDNO:7) was found to abrogate the migration of the U87R cells throughmembranes coated with a brain-like extracellular matrix (FIG. 2A). Otherphage peptides, e.g., M32 and M24, also showed a similar inhibitorytrend as H10, although not as strong an effect. The possibility thatbacterial components from the host culture could be causing theinhibition was ruled out by also testing the effects of LPS and a 20×volume of randomly selected phage. A synthetic version of the H10peptide was also able to inhibit the migration of U87R cells, as well asU87MG cells transfected with p75^(NTR) (FIG. 2B), a molecule shown to besufficient to confer a migratory phenotype in brain tumor xenografts[6]. These results confirmed the inhibitory property of this peptide inthe absence of the phage particle.

TABLE 1 U87R-binding peptides A2 SVSVGMKPSPRP (SEQ ID NO: 1) 21/100 M32GISLSSYLQSTQ (SEQ ID NO: 2) 20/100 C12 EHMALTYPFRPP (SEQ ID NO: 3)13/100 M5 HWAPSMYDYVSW (SEQ ID NO: 4)  7/100 M43 RTVPDYTAHVRT(SEQ ID NO: 5)  5/100 M19 SGHQLLLNKMPN (SEQ ID NO: 6)  4/100 H10TNSIWYTAPYMF (SEQ ID NO: 7)  3/100 F2 GMSLSRQMLWSL (SEQ ID NO: 8)  2/100M24 HLFPQSNYGGHS (SEQ ID NO: 9)  2/100 M23 CIQLANPPRLXG (SEQ ID NO: 10) 2/100

The global utility of the H10 peptide was tested in the transwell assayby using BTIC lines established from individual patient specimens. Asthese were isolated directly from resected tumors, it was felt theywould give an indication of the true clinical potential of H10. Themigration of 60% (3/5) of the BTIC lines tested was significantlyinhibited, although all five showed an inhibitory trend (FIG. 2C). Inexperiments where H10 had no significant effect, the cells were nothighly invasive to begin with.

B. H10 Affects the Turn Over of GM1-Containing Structures and OtherLipid Raft Components

To determine the molecular mechanism by which the H10 peptide isinhibiting glioma invasion, a biotinylated version of the peptide wasused to pull down potential binding partners which were then analyzed bymass spectrometry. Many of the proteins detected had some role orassociation with endosomal or vesicular transport (Table 2).

As lipid rafts are involved in some endocytotic processes [39-44], thereactions of the U87R cells to treatment with cholesterol oxidase, aknown lipid raft disruptor [45, 46], was examined. Cell migration wasabrogated in the transwell assay (FIG. 3A), and GM1, a component of bothnon-caveolar lipid rafts and caveolae [47, 48], was seen to accumulatewithin the cells, particularly at the plasma membrane (FIG. 3B). Similareffects were seen when cells were treated with H10, in comparison to acontrol phage, in three independent cell lines (FIG. 4A).

TABLE 2 Mass Spec Hits of Interest LIM Focal Domain Endosomes/Adhesions/CSK Containing Vesicle Plasminogen Reorganization: Proteins:Transport: Receptors: ESP-2 Zyxin RAB1B Alpha-enolase Zyxin ESP-2 RAB1AAnnexin A2 Gamma- TRIP6 MEL filamin Transgelin 2 Lasp-1 REB35 IQGAP1ABP-278 Rab-15 TRIP6 TIP47 Lasp-1 Clathrin ABP-278 Transferrin ReceptorProtein 1 Talin 1 Transmembrane protein 33 Glyceraldehyde-3- phosphatedehydrogenase SEC13 Coatomer protein complex

The p75 neurotrophin receptor (NTR) can be detected differentially inlipid rafts isolated with specific detergents [49]. Alternately,intracellular vesicles can deliver molecules required for a particularfunction to the polar extremes of a cell, for example, transport ofdigestive enzymes or structural molecules such as integrins to theleading edge during migration [50-52].

The p75^(NTR) can be detected differentially in lipid rafts isolatedwith specific detergents [49], and must be proteolytically processed totrigger cell migration in glioma cells [5]. Thus, it is probable thatp75^(NTR) is also cleaved within a lipid raft after endocytosis [53]. Todetermine if H10 may be having an impact on endosomally locatedp75^(NTR), cells were hypertonically lysed (to keep vesicles andorganelles at least partially intact) and separated on a 10-40%sucrose/iodixanol gradient from which fractions were individuallycollected. Both H10 and cholesterol oxidase resulted in a shift ofhigher molecular weight forms of p75^(NTR) into the denser gradientfractions (FIG. 4B). While the majority of p75^(NTR) does not appear tobe associated with GM1-containing lipid rafts, incubation of the cellswith H10 did cause increased co-localisation of the p75NTR intracellularand extracellular domains (FIG. 4C). Taken together, the data suggeststhat (i) H10 can inhibit the turn over of both GM1 andp75^(NTR)-containing lipid rafts and (ii) H10 appears to be preventingthe release of at least a portion of the p75^(NTR) extracellular domainproduced within a cell. In contrast, H10 and cholesterol oxidase have noeffect on the intracellular localization or gradient fractionation oftransferrin or its receptor, which are markers of clathrin-coatedvesicles (FIGS. 9A and 9B), and while H10 does not show an obviouseffect on the processing of over-expressed transfected p75^(NTR), it maycause a slight accumulation of endogenously expressed full lengthprotein (FIGS. 10A-10C).

III. BTIC-Cell Specific Peptides

A BTIC-specific phage library was generated as described for the 12Rlibrary, using U87MG cells, U251N cells, and human normal fetalastrocytes as subtraction cells to deplete the library of backgroundphage, and a mixture of BTIC isolates (BTIC 12, 25, 42, 50) fromdifferent patients for the selection.

A. Peptides from Phage Biopanned Against BTIC Isolates RevealHeterogeneity within Cultured Neurospheres.

The most abundant phage that was isolated was called 7A (25/50) andencoded the 12-mer sequence N-PSPHRQRQHILR-C (SEQ ID NO: 11). Inaddition, 5 other independent phage (10C, E10, 3F, C1 and 3B) wereisolated more than once and comprised 50% (25/50) of the subclonesscreened, shown in Table 3.

To confirm the preferential binding of 7A to the BTICs rather than thecells used for subtraction, neurospheres and U87MG cells were stained insuspension with biotin-labeled synthetic peptide. Two of the BTIC linesshowed a high percentage of positive cells within the neurosphere, whilenormal stem cells (not tumorigenic and not used in the depletion orselection) and U87MG cells were predominantly negative, as expected(FIG. 5B). Examination of the interaction of all selected peptidesacross a panel of BTIC lines underscored the heterogeneity within eachcell population, and established a platform for correlating the abilityto bind particular peptide sequences with either cell behavior orpatient outcome. FIG. 8 shows binding specificities of BTIC-specificpeptide hits on a representative selection of BTICs.

TABLE 3 BTIC-binding peptides 7A PSPHRQRQHILR (SEQ ID NO: 11) 25/50 10CQTIRIIIRRSRT (SEQ ID NO: 12)  6/50 E10 SLHMRHKRKPRR (SEQ ID NO: 13) 4/50 3F SSRSMQRTLIIS (SEQ ID NO: 14)  2/50 C1 IRSIRMRRILIL(SEQ ID NO: 15)  2/50 3B KTSMRPLILIHI (SEQ ID NO: 16)  2/50

As seen in FIG. 8, E10 binds to both U87MG and BTIC's, and has furtherbeen found to bind to both U87R (HIGC) and U87T (main tumor) cells.Thus, E10 can serve as a general marker for all three cell phenotypes ina GBM tumor.

IV. Homing Properties of the U87R and BTIC Binding Peptides

The ability of the selected phage or their corresponding peptides wasexamined for their ability to ‘home’ to their respective U87R or BTICglioma cell targets in vivo, according to their ability to detect gliomacells in an orthotopic xenograft model. In the case of H10, SCID micecarrying U87R or U87T xenografts were injected with the test phage forten minutes, which was subsequently perfused with PBS to remove anyunbound particles. Serial sections of the brains wereimmunohistochemically stained for M13 phage, demonstrating that H10homed specifically to the U87R, but not the U87T tumors (FIG. 6A).

To determine if 7A would also demonstrate binding specificity to asubset of cells within neurospheres in vivo, SCID mice carrying BTICxenografts were injected with 7A phage, and the brains cryosectioned foranti-phage immunohistochemistry. As seen with ex vivo staining ofneurospheres, only a subset of cells within the main tumor masses ofBTIC 12 and 25 showed positive staining (FIG. 6B). Additionally, nostaining was detected in the surrounding tissue as well as in xenograftsmade of non-target cells, specifically the U251N human glioblastomaline. Perfusion of a BTIC 25 xenograft with a control phage (Al,randomly selected subclone) showed minimal staining, again confirmingthe selectivity and binding specificity of the 7A displayed peptide.

The studies reported above indicate that 7A phage/peptide recognizesonly a subset of cells within an individual BTIC line (FIG. 5, FIG. 6B).It was therefore of interest to determine whether there were uniqueproperties of these cells of which 7A binding may be an indicator. TheBTIC 25 cells were subcloned by limiting dilution and screened forpeptide binding. The population of cells enriched for 7A binding wasdistinctly different from the non-binding counterparts, formingneurospheres in culture as opposed to adherent colonies (FIG. 7).Additionally, the 7A binding subpopulation did not proliferate well inorthotopic xenografts (3 months growth time), and could only be detectedin small numbers within the subventricular zone of the brain, a regionin the brain known to host a neural stem cell niche. The 7A non-bindingsubpopulation were very tumorigenic and formed very large tumor masseswith limited invasion into surrounding tissue. Therefore, the 7A peptidedistinguishes a population of cells associated with neurosphereformation, low proliferative activity in vivo, and a preference tolocate within the subventricular zone. The fact that both populationswere derived from a BTIC culture indicates that 7A is able to track theprogression of cells within this reservoir from hidden precursor torecurred tumor.

V. Peptide Composition and Peptide Conjugates

In one aspect, the invention includes a peptide composition fortargeting either (i) a highly invasive glioma cells (HIGC) subtype ofhuman GBM cells, e.g., the U87R subtype of U87GM cells, or (ii) a braintumor initiating cell (BTIC) subtype of human GBM cells, ascharacterized above. The peptide in the composition is 12-20 amino acidresidues in length and contains one of the sequences identified as SEQID NOS-1-17, or a sequence that is at least 90% homologous with thegiven sequence. That is, the peptide has the same sequence as one of SEQID NOS: 1-17, or a sequence that differs from the given sequence by atmost one amino acid residue. The peptide may contain only the givensequence of amino acids, or may contain additional N- and/or C-terminalresidues up to a total of 20 residues. Thus, for example, the peptidecorresponding to SEQ ID NO: 7, TNSIWYTAPYMF (H10), may have this exactsequence, the same sequence but with a single amino acid substitution,addition or deletion at any of the 12 residue positions, or a peptidehaving a total of up to eight additional residues at one or both of theN- or C-terminals. For example, SEQ ID NO:17 (KKGTNSIWYTAPYMF) containsthe 12 residues of SEQ ID NO: 7 (H10), plus three N-terminal residues(KKG) which make the H10 peptide substantially more water soluble byvirtue of the two additional lysine residues.

A. Peptides

The peptide of the invention is formed by conventional solid-phase orrecombinant DNA synthetic methods, using amino acids having the naturalL-isomer form, the D-amino acid form, or a mixture of the two. Peptideshaving an all D-form or partial D-form composition are expected to bemore resistant to proteolytic breakdown under biological conditions,e.g., when administered to a patient. Solid-phase peptide synthesismethods for preparing peptides composed of all L-amino acids, allD-amino acids or a mixture of D- and L-amino acids utilizing activatedD- or L-form amino acid reagents are described, for example, inGuichard, G., et al., Proc. Nat. Acad. Sci. USA Vol. 91, pp. 9765-9769,October 1994). Alternatively, the peptides may be composed of D-aminoacids synthesized in a reverse-sequence direction, that is, in a carboxyto amine end direction, to produce a so-called retro-inverso (RI) pilinpeptide. Methods for synthesizing RI-form peptides are detailed, forexample, in Fletcher, M. D. and Campbell, M. M., Partially ModifiedRetro-Inverso Peptides: Development, Synthesis, and ConformationalBehavior, Chem Rev, 1998, 98:763-795, which is incorporated herein byreference.

For use in targeting HIGCs, the peptide contains a sequence selectedfrom the group consisting of SEQ ID NOS: 1-10, 13, and 17, including SEQID NOS: 2 (M32), 7 (H10), and 9 (M24), of which SEQ ID NO: 7 (H10) isexemplary, 13 binds to both BTIC's, HIGC's and a population ofdifferentiated GMB tumor cells, and 17 is modified for enhancedsolubility. For use in targeting BTICs, the peptide contains a sequenceselected from the group consisting of SEQ ID NOS: 11-16, preferably SEQID NOS: 11(7A), 14 (3F) and 16 (3B), or which SEQ ID NO: 11 isexemplary.

B. Peptide Conjugates and Composition

For use as a diagnostic reagent, for detecting HIGC or BTIC subtypes ina patient with a human GBM tumor, the peptide may be coupled to acontrast agent, such as fluorescent moiety, for use in imaging GBM celltypes in vitro, or a contrast agent, for use in imaging GBM cell typesin vivo. Major imaging technologies that presently utilize contrastagents for in vivo imaging include x-ray/Computed Tomography (CT),Magnetic Resonance Imaging (MRI), Positron Emission

Tomography (PET), Single Photon Emission Computed Tomography (SPECT),and ultrasound technologies. Among widely used contrast agents are (i)gadolinium-based contrast agents, iron oxide contrast agents, andmanganese contrast agents used in MRI; ⁶⁴Cudiacetyl-bis(N⁴-methylthiosemicarbazone), ¹⁸F-fluorodeoxyglucose,¹⁸F-fluoride, 3′-deoxy-3′-[¹⁸F]fluorothymidine (FLT),¹⁸F-fluoromisonidazole, gallium, Technetium-99m, and thallium, used inPET or scintigraphy; and barium, gastrografin, and iodine contrastagents used in x-Ray imaging. The contrast agent or coordination complexcarrying the agent, e.g., a radio-isotopic metal, may be covalentlyattached to the peptide according to well known methods, e.g., through acovalently attached ligand coordination complex.

For use as a therapeutic agent, to inhibit or destroy HIGC or BTIC cellsspecifically, the peptide may be coupled to one or a variety ofanti-tumor agents, including, for example, alkylating agents,anti-metabolites, plant alkaloids and terpenoids, e.g. taxol,topoisomerases, proeosome inhibitors, and monoclonal antibodies. Theanti-tumor agents may be covalently attached to the peptide according towell-known methods. In another embodiment, the peptides are attached tothe surfaces of particles, e.g., liposomes, that carry the anti-tumoragent in encapsulated form.

In still another embodiment, the peptide of the invention is formed as afusion peptide with a peptide carrier, such as AngioPep-2 or AngioPep-7(SEQ ID NOS: 18 and 19, respectively) that is capable of facilitatingpassage of the peptide across the blood brain barrier (BBB) (62).

The composition of the invention may include (i) the peptide alone, (ii)the peptide in a suitable carrier, e.g., sterile physiological saline,in liquid or dried form, (iii) the peptide in coupled form as describedabove, or (iv) the peptide formulated in a suitable peptide-deliverynanoparticle, such as encapsulated within nanoparticles ofpoly(lactide-co-glycolide) copolymer, cyclodextrin nanoparticles, orcetyl alcohol/polysorbate. Nanoparticles useful for delivering drugsacross the BBB barrier are well known in the art (e.g., 68-71). Thenanoparticles are preferably in the 30-100 nm size range and may becoated with polyethyleneglycol for enhanced circulation time in thebloodstream. The particles may be suspended in an injectable medium,e.g., sterile physiological saline, or supplied in dehydrated form.

The peptide composition may contain multiple GBM binding peptides,and/or peptide conjugates, for example, at least one peptide or peptideconjugate that binds preferentially to BTIC's and at least one peptideor peptide conjugate that binds preferentially to HIGC's.

C. Carrier Peptide

Immunohistochemical staining of mouse brains carrying U87R tumors thathad been perfused with H10 phage showed positive signal that was eitherlocalized within the tumor mass or peritumoral, demonstrating that H10has the ability to cross the blood brain barrier (BBB). This feature isexploited, according to another aspect of the invention, in a novelcomposition comprising a conjugate of the H10 peptide, as a carrierpeptide, and a neuropharmaceutical or anti-cancer agent that is to bedelivered to the brain. The agent may include any pharmaceutical agentused, or potentially useful, in treating a neurological condition, suchas depression, anxiety, schizophrenia, hyperactivity, Alzheimer'sdisease, or Parkinson's disease, or any anti-tumor compound, such asfrom the classes named above, that would be effective against cancers ofthe brain or spine if the blood brain barrier could be breached. Theagent is coupled to the peptide according to known methods, such thoseinvolving direct attachment of the compound to an activated hydroxyl,sulfide, amine or carboxyl groups on the peptide or attachment of thepeptide to a corresponding activated group on the compound, or by theuse of a bifunctional coupling reagent.

VI. Diagnostic and Therapeutic Methods

Research into GBM has expanded from the biology of developed tumors intothe subsets of cells currently believed to be the initiators and diseasereservoirs for these tumors. The current view is that any given braintumor consists of a mixture of cells with varying stages of “sternness”or differentiation, with each subpopulation retaining inherentpotentials to contribute to relapse [1, 54]. New microarray data havebegun to better delineate profiles for predicting patient outcome, andthe nature of recurrent disease [1]. It is becoming evident that not allof these subpopulations are treatable by current therapeutics,ultimately resulting in relapsed disease. Further complicating thescenario, these cell populations may also be stimulated by chemo- andradiotherapy to evolve into more aggressive phenotypes [55, 56]. Onegoal of the present invention is to contribute to the practical solutionof eliminating the identified subtypes of GBM and associated diseasereservoirs.

To that end, the invention provides methods for diagnosis and/ortreating patients with human GBM tumors, and in particular, provides animprovement in the treatment of GBM tumors in human patients, bycharacterizing and/or treating subpopulations of tumor cells that arelikely causes of tumor recurrence. The patient may have been previouslytreated with one or more known treatment modalities, such aschemotherapy, x-radiation therapy and/or surgical resection. The initialtreatment may cause a significant reduction in tumor size or growth, butthe tumor may likely recur due to the presence of a HIGC subpopulationof cells that may reside outside the treatment region, or through a BTICsubpopulation of cells capable of reseeding the tumor with activelydividing GBM cells

A. Method of Characterizing a GBM Tumor

In one aspect, the invention provides a method of characterizing aglioblastoma multiforme (GBM) tumor in a patient according to thedensity and distribution of different cell phenotypes within the tumor,including the HIGC and BTIC phenotypes, associated with tumor reservoirthat may escape current treatment methods.

The method involves generating one or more images of the patient's braintumor that indicates the density and distribution of both HIGC and BTICsubtypes within the tumor region, and optionally, the maindifferentiated tumor cells making up the majority of the tumor. Where asingle image is formed, the patient is administered a cocktail(multiple-peptide composition) of two or more single-peptidecompositions, one containing a peptide that preferentially targets HIGCcells and is coupled to a first contrast agent, and the secondcontaining a peptide that targets BTIC cells and is coupled to a secondcontrast agent, where the two contrast agents allow visualization ofbinding to each peptide to its target cell type. Where two or moreseparate images are formed, for visualizing the distribution of the twoor more cell types separately, an individual image is formed afteradministration of each peptide composition. In this embodiment, the samecontrast agent may be used for each image. The separate images can beintegrated into a single image by known image processing techniques.

The techniques that may be used include magnetic resonance imaging(MRI), positron emission tomography (PET), scintigraphy, computedtomography (CT), and x-ray. For each technique, a variety of suitablecontrast agents are available, including (i) gadolinium-based contrastagents, iron oxide contrast agents, and manganese contrast agents usedin MRI; ⁶⁴Cu diacetyl-bis(N⁴-methylthiosemicarbazone),¹⁸F-fluorodeoxyglucose, ¹⁸F-fluoride, 3′-deoxy-3′-[¹⁸F]fluorothymidine(FLT), ¹⁸F-fluoromisonidazole, gallium, Technetium-99m, and thallium,used in PET or scintigraphy; and barium, gastrografin, and iodinecontrast agents used in x-ray imaging. The contrast agents may becoupled to the associated peptide by standard methods, such as directcovalent coupling, or for radio-imaging metals, covalent coupling of ametal chelate to the peptide.

With the one or more images thus generated, the physician can readilyassess the density and distribution, e.g., localization of the first andsecond peptides and their associated contrast agent within the tumor andat the margins of the tumor.

FIGS. 13-19 demonstrate in vivo targeting to BTIC- and HIGC-specificpeptides to specific cells of a human GBM tumor implanted in a mousebrain. In the studies shown in FIGS. 13A and 13B, brain tumors wereimplanted in mice with a patient-derived BTIC cell line BT025 identifiedas above by its binding to the 7A peptide. After tumor growth from theimplanted cells, the tumors were removed, sectioned and stained formicroscopic visualization. In the studies shown in FIGS. 14-19, afluorescent peptide was administered intravenously, either byintracorotid injection or via tail vein into mice having an implantedGBM tumor from the BT025 cell line (FIGS. 14-17) or the U87MG cell line(FIGS. 18 and 19), and after localization of the peptide, the animalwere sacrificed and their brain tumors removed for sectioning andvisualization by fluorescence microscopy. The results of these studiesdemonstrate that, for each peptide tested, a fluorescent conjugate ofthe peptide, when administered intravenously, was able to targetspecific brain tumor cells.

FIG. 13A shows high magnification images of thin sections from fivemouse brains that were previously injected with the BT025 cell line, andstained with antibodies specific to an antigen present only in humannuclei, and a dark brown detection reagent. The figure confirms thediffusion of 7A binding cells through the brain tissue.

FIG. 13B shows thin sections from five separate mouse brains injectedwith the BT025 subclones. The toluidine blue staining clearly showsmassive tumor growth and disruption of normal tissue architecture. Thus,7A binding in vitro prior to injection of the cells into mouse brainscan predict the in vivo behaviour of the different BT025 cellsubpopulations.

FIG. 14A shows the ability of fluorescently labeled 7A peptide (SEQ IDNO: 11, preferential for BTIC binding) to home in a live mouse to alarge implanted tumor grown from BT025 cells. The peptide wasadministered to the mouse via intracarotid injection and allowed tocirculate for approximately half an hour to allow clearance ofbackground signal before the mouse was sacrificed and the brain removedfor imaging using an Olympus OV100 whole mouse imaging system. Bynon-magnified inspection, the large outgrowth of the tumor is obvious.(FIG. 14A) The fluorescent signal appears strongly in part of the tumor,but clearly does not detect all tumor cells present.

FIGS. 14B and 14C are lower and higher magnification photomicrographs ofa thin section taken from the brain in FIG. 14A after it was bisectedclose to the tumor implantation site and stained for human nuclearantigen (green) and total DNA (blue) to outline the positioning of thecells. The red peptide signal is visible on cells immediately adjacentto the main tumor mass as well as spread diffusely in the surroundingtissue. FIG. 14C in particular, shows that the 7A peptide bindsprimarily to cells that are diffusely spread outside the main tumormass.

FIGS. 15A and 15B show similar sections views, where the animal wasinjected with a fluorescently labeled 3B peptide (SEQ ID NO: 16, alsopreferential for BTIC cell binding). FIG. 15B shows that 3B binds tocells that are both within and outside the main tumor mass. Thisindicates that 3B can detect both proliferative and diffusely migratorytumor cell populations.

FIGS. 16A and 16B show similar views, where the animal was injected witha fluorescently labeled 3F peptide (SEQ ID NO: 14, also preferential forBTIC cell binding). FIG. 16B shows that when thin sectioned, most of thered signal appears outside of the main tumor mass, but close to thegreen signal for human nuclear antigen on cells that have diffuselymigrated in the surrounding tissue. FIGS. 17A and 17B shows that similarresults can be obtained when the peptide is administered by tail veininjection rather than intracarotid.

FIGS. 18A and 18B-18D show similar views, where the animal was injectedwith a fluorescently labeled modified H10 peptide (SEQ ID NO: 17,preferential for HIGC binding), in animals carrying a tumor initiatedwith the U87MG human glioblastoma cell line. For these studies, thetumors were not grown as large, and a far-red fluorescent signal is notobvious from inspection without sectioning (FIG. 18A). FIG. 18B-18C(different magnifications of the same section) show that the modifiedH10 peptide binds primarily to cells that are diffusely spread outsidethe main tumor mass, as would be expected of HIGC's. A similar resultwas seen when the peptide was injected via a tail vein (FIG. 18D).

FIGS. 19A and 19B and 19D show similar views, where the animal wasinjected with a fluorescently labeled modified E10 peptide (SEQ ID NO:13, which binds to both BTIC's and HIGC's), in animals carrying a tumorinitiated with the U87MG human glioblastoma cell line. For thesestudies, the tumors were not grown as large, and a far-red fluorescentsignal is not obvious from inspection without sectioning (FIG. 19A).FIG. 19B shows that E10 binds to a portion of cells within the maintumor mass, and FIG. 19C shows that E10 also binds to cells outside ofthe main tumor mass. Similar results were obtained when the peptide wasadministered via the tail vein.

The studies reported above show that peptide conjugates specific forBTICs (7A, 3B, and 3F), for HIGC's (modified H10), and for both celltypes (E10), can localize in human GBM tissue in vivo to provideinformation on the density and localization of the various cell types invivo, and that targeting can be carried out by intravenousadministration of the peptide conjugate.

It can be appreciated from the images obtained how the method can beused to determine the dimensions and coordinates of the tumor, both themain tumor and the tumor margin that may contain reservoir cells,particularly HIGC's but also BTIC's. This information, in turn, willallow the surgeon to better define the margins of the tumor that need tobe removed in order to reduce the risk of relapse, and will allow theradiation oncologist to more accurately define the brain volume andcoordinates that need to be included in the radiation treatment.

Since the progress of a treatment regimen will need to take into accountthe presence and distribution of reservoirs tumor cells, the method canalso be used to monitor the effectiveness of treatment in eliminating orreducing reservoir cells. In this embodiment, the brain may be imaged inaccordance with the method at an initial time zero, then reimaged at oneor more times over the course of the treatment, to track the effect ofthe tumor on reservoir cells.

Finally, the treatment method may be used to tailoring a chemotherapyfor GBM tumor therapy, using the different expression profiles ofdifferent tumor-cell phenotypes within the tumor. FIG. 20 show geneclustering of microarray data generated from mRNA isolated from threeindependently isolated 7A binding cell subclones and three independentlyisolated 7A non-binding subclones. The gene expression profiles of allthe 7A binding subclones clustered together (demonstrating similar geneexpression), as did the 7A non-binding subclones. This strengthens thenotion that 7A distinguishes between BTIC subtypes that aretranscriptionally unique, and whose behavior in vivo can be predicted.The gene expression data may allow the oncologist to examine thedifferent gene expression profiles of cells in identifyingchemotherapeutic agents that are most effective against particular geneexpression profiles.

B. Gene Expression Profiling

In accordance with another aspect of the invention, the discovery ofpeptides that bind preferentially to particular peptides to GBM cellsubtypes that in turn have different gene expression profiles provides anovel method for characterizing a tumor in terms of its component cells.According to this method, the oncologist would correlate the identifiedcell type with the known gene expression pattern of that cell type, thendetermine the presence and/or distribution and/or number of cells ofeach particular type with the peptides of the invention, as a basis fortailoring the therapy to a known identified gene expression profile.

C. Therapy

In still another aspect, the peptide composition of the invention areuseful for targeting therapeutic agents to particular tumor cell typesfor tumor treatment. As one general strategy, the oncologist might adoptone known therapy, e.g., surgery, radiation, or chemotherapy or acombination of these, for treating the tumor, and secondarily use thepeptide composition of the invention to target therapeutic agents to thereservoir cells of the tumor, to minimize the reservoir effect inrelapse after the initial treatment.

A number of delivery system are available for delivering the peptidecomposition to the brain (62-71), including intravenous administration.As noted above, the H10 peptide is itself able to pass the blood brainbarrier, and so may be administered by any systemic route includingintra-arterial, IV, IM, subQ, nasal, mucosal or through the lungs,either as a peptide alone or peptide coupled to an imaging or ananti-tumor agent. The studies conducted on mice tumor further shows thatall of the peptides studied were able to target brain tissue followingintravenous administration.

Other available strategies for CNS delivery may be broadly classified aseither invasive (neurosurgical-based), such as convection-enhanceddelivery (66), pharmacologic-based, or physiologic-based (63).Neurosurgical-based strategies include intraventricular drug infusion,intracerebral implants, and BBB disruption. Pharmacologic-basedstrategies include the use of nanoparticle carriers (described, forexample, in 68-71). Physiologic-based strategies take advantage of thenormal, endogenous pathways of either carrier-mediated transport ofnutrients or receptor-mediated transport of peptides.

In the latter category, Drappatz et al. conducted a Phase I study ofANG1005 in patients with recurrent glioblastomas. ANG1005 consists ofthree paclitaxel molecules linked to a novel peptide, Angio-Pep-2, thatallows it to be transported across the blood-brain barrier via thelow-density lipoprotein receptor-related protein 1 receptor (62).Angio-pep-2 is 19-amino acid peptide (SEQ ID NO: 17) that binds to lowdensity lipoprotein receptor-related protein (LRP) receptors at the BBBand has the potential to deliver drugs to brain by receptor-mediatedtransport. Here the BTIC- or HIGC-specific peptide, with or withoutassociated radio-imaging or anti-tumor agent, is coupled to theAngio-pep peptide, and delivered by a systemic route.

Alternatively, after completing surgery to remove the primary tumor, thecomposition of the invention can be administered either directly inwafers or by installing a convection enhanced delivery pump to deliverthe peptides on a routine schedule. Convection-enhanced delivery (CED)uses an infusion catheter whose tip is placed close to the target site.In this technique, a cannula is inserted directly into the area of thebrain to be treated, and the therapeutic agent is delivered through thecannula via bulk flow, circumventing the BBB.

The peptide composition could alternatively be administered after briefdisruption of the BBB using mannitol or other BBB disruption agent. Thisapproach has recently been used to deliver Avastin to the brain tumorsof patients (67).

Still another delivery method uses nasal transport routes via theolfactory nerve pathway (axonal transport) and the olfactory epithelialpathway.

As indicated above, the diagnostic method is carried out to imagereservoirs of BTICs and/or HIGCs, typically after an initial treatmentof the GBM tumor, e.g., by surgery, radiation therapy or chemotherapy.Depending on the resolution in visualizing targeted cells, the dose ofdiagnostic composition administered to the patient, or the route ofadministration, may be varied until a meaningful diagnostic result isobtained.

After identifying reservoirs of either cell type, the patient may betreated with the peptide in therapeutic form, to knock out or reducepopulations of the reservoir cells. During this treatment, progress inreducing HIGC or BTIC populations can be checked periodically with thediagnostic method, and the therapeutic dose of the composition may bevaried, if necessary, to increase the extent of inhibition ordestruction of the targeted HIGCs or BTICs. Treatment is continued,e.g., by twice weekly or weekly administration of the composition, untila desired endpoint is observed.

The experimental procedures described below are exemplary, and in no wayintended the scope of the invention as defined by the claims.

VII. Experimental Procedures:

All animal experiments were conducted in accordance with the approvaldocuments provided by the University of Calgary Ethics Board and AnimalCare Facility. Tumor and normal tissues including the isolation of braintumor initiating cell from banked patients' samples were obtained fromthe Tumor Tissue Bank in Foothills Hospital, Calgary, Alberta.

A. Cell Culture:

The human glioma cell line U87 was obtained from the American TypeCulture Collection, transfected with GFP and separated into the U87T andU87R subpopulations as previously described [6]. The human glioma cellline U251N and human fetal astrocytes were a kind gift from V. W. Yong(University of Calgary, Calgary, Alberta, Canada). All cells weremaintained in complete media (Dulbecco's modified eagle's medium [DMEM]supplemented with 10% heat-inactivated fetal bovine serum [FBS], 0.1 mMnonessential amino acids, 2 mM L-glutamine, 1 mM sodium pyruvate, andtransfected cells with 400 μg/ml of G418 (Invitrogen) at 37° C. in ahumidified 5% CO₂ incubator. Cells were passaged by harvesting withtrypsin (Gibco BRL) at 80%-90% confluence.

Brain tumour initiating cells (BTICs) were supplied by the BTIC CoreFacility, maintained by Drs. Greg Cairncross and Samuel Weiss, afterisolation by Dr. John Kelly [28] and maintained in NeuroCult media (StemCell Technologies) as neurospheres. Subcloning of the BTIC25 line into7A positive and negative populations was done by limiting dilution.

B. Bacteriophage Culture:

The Ph.D.^(TM)-12 Phage Display Peptide Library Kit (New EnglandBiolabs) was used as per manufacturer's protocol. Briefly, phagelibraries were amplified as follows: Overnight cultures of the bacterialhost strain ER2738 were diluted 1/100 in LB broth with 20 μg/mLtetracycline and inoculated with 10 μL of phage (˜10⁸-10¹⁰ pfu/μL), thencultured with shaking at 37° C. overnight. Bacteria were pelleted andthe phage were precipitated from the supernatant by adding 1/6 volume of20% w/v PEG-8000, 2.5M NaCl and storing at 4° C. overnight, followed bycentrifugation for 15 minutes at 10000×g. The pellet contained phage andwas reconstituted in PBS. Purified phage were put through a 0.22 μmfilter if intended for mouse work.

Phage titers were determined by adding 10 μL of serially diluted phageand 200 μL of ER2738 to 3 mL of 7% agarose in LB warmed to 50° C., andpoured over a warmed plate of LB agar with 20 μg/mL tetracycline 40μg/mL XGal and 50 μg/mL IPTG. After overnight culture at 37° C., blueplaques were counted for calculation of pfu/μL. Plaques could besubcloned by removing an isolated plaque from the agar plate using aPasteur pipette and extracting the phage in 100 μL of 20 mM Tris-HCl pH8.0, 100 mM NaCl, 6 mM MgSO₄ at 4° C. overnight. Amplification cultureswere inoculated with 20 μL of the extraction buffer, as described above.

C. Biopanning for U87R (Invasive Glioma)-Specific Peptide Sequences:

Biopanning was performed as described in [61]. Subtraction cells (e.g.U87T) were released from tissue culture plastic with Puck's EDTA, andafter washing with PBS, 1×10⁷ cells were resuspended in 1% BSA in PBSwith 1.5×10¹¹ pfu of Ph.D.-12 M13 Phage Library (New England Biolabs).The cells and phage were incubated in an eppendorf tube for 1 hour atroom temperature with gentle shaking, before pelleting the cells andretaining the supernatant, which was transferred to a fresh tube withanother aliquot of subtraction cells. The incubation and transfer ofsupernatant was performed three times, with the supernatant beingtransferred to an empty tube on the last round. Selection cells werereleased from tissue culture plastic with Puck's EDTA (e.g. U87R cells)and washed in PBS. 5×10⁶ cells were resuspended in the 3× subtractedsupernatant and incubated for 4 hours at 4° C. with slow shaking Thecell pellet was washed 5× in cold 1% BSA/0.1% Tween 20 in PBS fivetimes, changing the tube after each wash. Bound phage were eluted byrocking the cells gently for 10 minutes at 4° C. in 1 mL of 0.2MGlycine-HCl pH 2.2 with 1 mg/mL BSA, and the supernatant was immediatelyneutralized with 150 μL of 1M Tris-HCl pH 9.1. The final library wasamplified as per manufacturer's protocol.

D. Biopanning for BTIC-Specific Peptide Sequences:

A BTIC-specific phage library was generated as described for the U87Rlibrary, this time using U87MG cells, U251N cells, and human normalfetal astrocytes to deplete the library of background phage, and amixture of BTIC cell lines from different patients were used for theselection. Cells were released with EDTA if adherent, or if grown asneurospheres (e.g. BTIC cells) were separated into single cells byrepeated pipetting through a small bore pipette tip. Otherwise, thesubtractive and selective biopanning were performed as described for theU87R library.

E. Whole Cell ELISA:

1×10⁴ test cells were plated into a well of a 24-well dish, in 0.5 mL ofmedia and allowed to equilibrate overnight under normal cultureconditions, then the media was replaced with HEPES-buffered culturemedia. 5×10⁹ pfu phage were added to the wells with gentle shaking for 1hour at room temperature followed by three washes with PBS. Bound phagewere detected with anti-M13-HRP antibody (GE Healthcare) and insolubleTMB substrate (Sigma).

F. Transwell Assays:

The membranes of 8 μm pore sized transwell inserts (Corning Costar) werecoated with brain-like matrix (720 μL of 3 mg/mL collagen I (PureCol);1804, of 10× DMEM (Invitrogen); 9 uL of 1 mg/mL human plasma fibronectin(Sigma); 9 uL of 1 mg/mL chondroitin sulfate proteoglycans (Chemicon);16 μL of 0.15 mg/mL laminin (Chemicon)) on both sides, allowed to dry,then plated with 5×10⁴ cells in 100 μL media in the upper chamber and500 μL media in the lower chamber. Inclusion of collagen was essentialto see the inhibitory effect of H10 (Fig. S4). 3×10¹⁰ pfu of test phagewere added to the upper chambers containing the cells, which wereincubated for 4 hours under normal culture conditions. At the end of theincubation, the media was aspirated and the cells were fixed and stainedin 1% crystal violet in 95% ethanol for one minute. Transwells wererinsed in PBS, then cells on the upper membrane surfaces were removedwith a cotton swab. Cells which had migrated to the undersurface of themembranes were counted by light microscopy, and the sum of cells in fivemicroscopic fields was recorded for each membrane.

G. Confocal Microscopy:

Adherent cells: 13 mm coverslips were coated with neutralized 3 mg/mLCollagen I (PureCol), allowed to dry, then plated with test cells at1×10⁴/mL, 0.5 mL volume and allowed to equilibrate 20 minutes undernormal culture conditions. Coverslips were fixed for 10 minutes in 3%formaldehyde in PBS, washed, then incubated in biotinylated peptide (3mM stock) or primary antibody at a 1:100 dilution in 2% BSA/0.02% Tween20 in PBS for 1 hour at room temperature. After washing in PBS,secondary antibody or streptavidin-Alexa 568 was applied at a dilutionof 1:250 for 1 hour before coverslips were washed and mounted with DAKOmounting media with antifade.

Suspended neurospheres: 504, of densely suspended neurospheres werestained as described above, except in suspension in an eppendorf tube.The stained neurospheres were mounted in a drop of DAKO mounting mediaunder a coverslip.

H. In Vivo Phage Homing

3×10⁴ U87T or 3×10⁵ U87R cells were injected in a 34 volume into onebrain hemisphere of a SCID mouse and allowed to grow for 4 or 6 weeksrespectively. For specific molecular staining, unlabeled primaryantibodies, FITC-transferrin or A1exa555-cholera toxin B subunit(Invitrogen) were diluted 1:100 in 2% BSA/0.02% Tween 20 in PBS and usedin place of biotinylated peptides. When needed, species-specificfluorescently labeled secondary antibodies (Molecular Probes,Invitrogen) were diluted 1:500. Primary antibodies used includedanti-p75 intracellular domain pAb (Promega), anti-p75 extracellulardomain mAb clone ME20.4 (Cell Signaling, Millipore), andanti-transferrin receptor (Invitrogen).

I. Sucrose/Iodixanol Gradients:

Cells were scraped into 1 mL of 0.25M sucrose, 140 mM NaCl, 1 mM EDTA,20 mM Tris-HCl, pH 8.0, and dounce homogenized until cells were nolonger visible by microscopy. Debris was pelleted for 5 min, 800×g andthe supernatant was loaded on top of a 10 mL continuous 10-40% gradient,prepared by the dilution of OptiPrep (Sigma, 60% iodixanol) with 0.25Msucrose, 140 mM NaCl, 3 mM EDTA, 60 mM Tris-HCl, pH8.0. Gradients werespun in a swinging bucket rotor at 48000×g for 18 hrs and 0.5 mLfractions were collected. Total protein was precipitated from eachfraction by the addition of 2 volumes of −20° C. 20 mM DTT, 15% TCA,storage at −20° C. overnight, followed by centrifugation at 4° C. for 20minutes. Pellets were resuspended in 20 μL 1M Tris and 20 μL 2× Laemmlibuffer. The entire volume was loaded into a single well for SDS-PAGEresolution and western transfer.

J. In Vivo Phage Homing:

3×10⁴ U87T cells, 3×10⁵ U87R cells or 5×10⁴ BTICs were injected in a 34volume into one brain hemisphere of a SCID mouse and allowed to grow for4, 6 or 12 weeks respectively. The mice were anaesthetized, then treatedwith 150 μL of 20% (w/v) mannitol for 15 minutes before injecting 5×10⁹pfu into the brain via the carotid. After allowing the phage tocirculate for 10 minutes, unbound phage were flushed out of thecirculatory system with 15 mL of PBS injected into the left ventricleafter the right atrium was clipped. The brains were harvested,immediately frozen on dry ice and embedded in OCT for sectioning.

K. Immunohistochemistry:

Serial sections were fixed with cold acetone, and rehydrated through anethanol gradient. Endogenous peroxidases in the sections wereinactivated with 0.075% H₂O₂/methanol, and nonspecific binding wasblocked with 10% normal goat serum in PBS. The sections were incubatedwith 1:100 diluted rabbit polyclonal anti-M13 antibody (in house), or1:50 diluted mouse monoclonal anti-human nuclei (Chemicon) in blockingbuffer. Following washing with PBS, the appropriate biotinylatedsecondary antibody (Vector Laboratories, http://www.vectorlabs.com) wasapplied. Avidin-biotin peroxidase complexes were then formed using theVECTASTAIN Elite ABC kit (Vector Laboratories) and detected by additionof SIGMAFAST DAB (3,39-diaminobenzidine tetrahydrochloride)(Sigma-Aldrich), which was converted to a brown reaction product by theperoxidase. Toluidine blue (for frozen sections) was used as a nuclearcounterstain. Sections were then dehydrated in an ethanol/xylene seriesand mounted with Entellan (Electron Microscopy Sciences).

SEQUENCE LISTING

SVSVGMKPSPRP (SEQ ID NO: 1) (A2) GISLSSYLQSTQ (SEQ ID NO: 2) (M32)EHMALTYPFRPP (SEQ ID NO: 3) (C12) HWAPSMYDYVSW (SEQ ID NO: 4) (M5)RTVPDYTAHVRT (SEQ ID NO: 5) (M43) SGHQLLLNKMPN (SEQ ID NO: 6) (M19)TNSIWYTAPYMF (SEQ ID NO: 7) (H10) GMSLSRQMLWSL (SEQ ID NO: 8) (F2)HLFPQSNYGGHS (SEQ ID NO: 9) (M24) CIQLANPPRLXG (SEQ ID NO: 10) (M23)PSPHRQRQHILR (SEQ ID NO: 11) (7A) QTIRIIIRRSRT (SEQ ID NO: 12) (10C)SLHMRHKRKPRR (SEQ ID NO: 13) (E10) SSRSMQRTLIIS (SEQ ID NO: 14) (3F)IRSIRMRRILIL (SEQ ID NO: 15) (C1) KTSMRPLILIHI (SEQ ID NO: 16) (3B)KKGTNSIWYTAPYMF (SEQ ID NO: 17) (Modified H10) TFFYGGSRGKRNNFKTEEY(SEQ ID NO: 18) (AngioPep-2) TFFYGGSRGRRNNFRTEEY (SEQ ID NO: 19)AngioPep-7)

1. A peptide composition for targeting one of (i) a highly invasiveglioma cell (HIGC) subtype of human glioblastoma multiforme (GBM) cellscharacterized by their ability to migrate from one brain hemisphere intowhich the cells are injected into the contralateral hemisphere, and (ii)a brain tumor initiating cell (BTIC) subtype of human GBM cellscharacterized by their stem-cell like properties of being able to selfrenew, generate spheres without the addition of exogenous mitogens andgrowth factors, and induce tumor formation in vivo when placed in thebrains of immuno-compromised mice, comprising an isolated peptide havingbetween 12-20 amino acids, and containing a sequence selected from thegroup consisting of SEQ ID NOS: 1-10, 13, and 17 for targeting HIGCs,and SEQ ID NOS: 11-16, for targeting BTICs.
 2. The peptide compositionof claim 1, wherein the peptide is composed of L-amino acids, D-aminoacids, a mixture of L- and D-amino acids, or a retro-inverso peptideformed of D-amino acids arranged in reverse order.
 3. The peptidecomposition of claim 1, for use in localizing of HIGCs or BTICs in asubject with a human GBM tumor, which further includes a contrast agentattached to the peptide.
 4. The peptide composition of claim 1, for usein inhibiting or killing HIGCs or BTICs in a subject with a human GBMtumor, which further includes an anti-tumor agent attached to thepeptide.
 5. The peptide composition of claim 1, for use in targetingHIGCs, wherein the peptide contains a sequence selected from the groupconsisting of SEQ ID NOS: 7 (H10), 13 (E10) and 17 (modified H10); 6.The peptide composition of claim 1, for use in targeting HIGCs, whereinthe peptide contains the sequence identified by SEQ ID NOS: 17 (modifiedH10);
 7. The peptide of composition 1, for use in targeting BTICs,wherein the peptide contains a sequence selected from the groupconsisting SEQ ID NOS: 11 (7A), 13 (E10), 14 (3F) and 16 (3B).
 8. Thepeptide composition of claim 7, wherein the peptide has the sequenceidentified by SEQ ID NOS: 11 (7A).
 9. The peptide composition of claim1, for use in delivery to a patient human GBM tumor across theblood-brain barrier, wherein the peptide is coupled to a carrier peptidehaving the sequence identified by SEQ ID NOS: 18 or
 19. 10. The peptidecomposition of claim 1, wherein the peptide is encapsulated within ananoparticle formed of poly(lactide-co-glycolide) copolymer, acyclodextrin, or cetyl alcohol/polysorbate.
 11. The peptide compositionof claim 1 which includes at least one peptide that binds preferentiallyto HGIC's and at least one peptide that binds preferentially to BTIC's.12. The use of the composition of claim 1, for detecting the presence ofHIGC or BTIC subtypes of cells in a patient with GBM tumor, where thecomposition includes a detectable contrast agent coupled to the peptide.13. The use of the peptide composition of claim 1, for inhibiting orkilling HIGC or BTIC subtypes of cells in a patient with GBM tumor,where the composition includes an anti-tumor agent coupled to thepeptide.
 14. A method of characterizing a glioblastoma multiforme (GBM)tumor in a patient, comprising (a) generating an image of the patient'sbrain tumor after administering to the patient a peptide compositioncontaining (i) a first peptide having between 12-20 amino acids inlength that has been selected for its preferential binding to a highlyinvasive glioma cell (HIGC) subtype of human GBM cells characterized bytheir ability to migrate from one brain hemisphere into which the cellsare injected into the contralateral hemisphere, and coupled to firstpeptide, a first contrast agent that allows the first peptide, whenbound to cells in the patient tumor region, to be imaged in vivo; (b)generating an image of the patient's brain tumor after administering tothe patient a peptide composition containing (i) second peptide havingbetween 12-20 amino acids in length that has been selected for itspreferential binding to a brain tumor initiating cell (BTIC) subtype ofhuman GBM cells characterized by their stem-cell like properties ofbeing able to self renew, generate spheres without the addition ofexogenous mitogens and growth factors, and induce tumor formation invivo when placed in the brains of immunocompromised mice, and coupled tothe second peptide, a second contrast agent that allows the secondpeptide, when bound to cells in the patient tumor region, to be imaginedin vivo; (c) determining, from the distribution of the first and secondpeptides and their associated contrast observed in the image(s)generated in steps (a) and (b), at least one of: (ci) the boundaries ofthe tumor, for purposes of surgical resection of the tumor, (cii) theboundaries of the tumor for purposes of radiation therapy of the tumor,(ciii) the expression profiles of different tumor-cell phenotypes withinthe tumor, for purposes of tailoring a chemotherapeutic regimen fortreating the tumor; and (civ) the change in the distribution of thefirst and second peptides and their associated contrast agents over agiven time course in which steps (a) and (b) are repeated over time. 15.The method of claim 14, wherein steps (a) and (b) are carried out by oneof: (i) MRI, wherein the contrast agent is selected from the groupconsisting of a gadolinium-based contrast agent, an iron oxide contrastagent, and a manganese contrast agent; (ii) positron emission tomography(PET) or scintigraphy, wherein the contrast agent is selected from thegroup consisting of ⁶⁴Cu diacetyl-bis(N⁴-methylthiosemicarbazone),¹⁸F-fluorodeoxyglucose, ¹⁸F-fluoride, 3′-deoxy-3′-[¹⁸F]fluorothymidine(FLT), ¹⁸F-fluoromisonidazole, gallium, Technetium-99m, and thallium;and (iii) x-ray imaging, where the contrast agent is selected from thegroup consisting of barium, gastrografin, and iodine contrast agents.16. The method of claim 14, wherein steps (a) and (b) are carried outtogether and the first and second contrast agents allow thedistributions of bound first and second peptides to be independentlydetermined.
 17. The method of claim 14, wherein steps (a) and (b) arecarried sequentially.
 18. The method of claim 14, wherein the firstpeptide contains a sequence selected from the group consisting of SEQ IDNOS: 7 (H10), 13 (E10) and 17 (modified H10);
 19. The method of claim14, wherein the second peptide contains a sequence selected from thegroup consisting SEQ ID NOS: 11 (7A), 13 (E10), 14 (3F) and 16 (3B). 20.The method of claim 14, wherein said peptide compositions areadministered intravenously.
 21. A method of characterizing the geneexpression profiles of cellular phenotypes in a human glioblastomamultiforme (GBM) tumor in a patient, comprising (a) identifying cells inthe tumor corresponding to one of (i) a differentiated GBM tumor cell,(ii) a highly invasive glioma cell (HIGC) subtype of human glioblastomamultiforme (GBM) cells characterized by their ability to migrate fromone brain hemisphere into which the cells are injected into thecontralateral hemisphere, and (iii) a brain tumor initiating cell (BTIC)subtype of human GBM cells characterized by their stem-cell likeproperties of being able to self renew, generate spheres without theaddition of exogenous mitogens and growth factors, and induce tumorformation in vivo when placed in the brains of immuno-compromised mice,and (b) correlating the identified cell type with the known geneexpression pattern of that cell type.